Installing AFNI on Mac OS X 10.11 “El Capitain”

We’ve all been there, Apple releases a new Operating System and when you install it, you find out that your favorite programs don’t work on launch day or require some special install instructions.  Well if you’ve installed AFNI onto a Mac running 10.11, you may notice that some of the Python programs don’t fully work.  This isn’t AFNI’s fault, it’s actually a “subtle” change in the OS that limits the abilities of interpreters (like Python) to gain access to shell variables (like DYLD_*).

So how do you actually go about installing AFNI on a system running 10.11.x?  Well you have (like always) plenty of options, but my preferred way to do it uses *surprise* homebrew.

1. Install Xcode via the Mac App Store
2. Install Homebrew
3. Install GCC via Homebrew

brew install gcc --with-all-languages --without-multilib

4. Install PyQT (for access to uber_subject.py and uber_ttest.py)

brew install pyqt

5. Link your libgomp.1.dylib to the correct location for AFNI to find it.  Note that you’ll want to look for this file and not just copy the command below:

ln -s /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/libgomp.1.dylib /usr/local/lib/libgomp.1.dylib

6. Install glib

brew install glib

7. Download AFNI’s 10.7 binaries and move to ~/abin
8. Setup your path

echo "export PATH=$PATH:~/abin"

9. Test your setup

afni_system_check.py -check_all

10. Rejoice.

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